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    Correction to: primary antibody deficiencies in Turkey: molecular and clinical aspects
    (Springer, 2021) Fırtına, Sinem; Ng, Yuk Yin; Ng, Özden H.; Kıykım, Ayça; Yücel Özek, Esra; Kara, Emine Manolya; Kaya, Ayşenur
    The original published version of this article contained a mistake in one of the affiliations. The correct affiliation of author Manolya Kara (7) should read: Istinye University Faculty of Medicine, VM MedicalPark Pendik Hospital, Pediatric Infectious Diseases Clinic, Istanbul, Turkey The original article has been corrected. © 2021, Springer Science+Business Media, LLC, part of Springer Nature.
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    Determining T and B Cell development by TREC/KREC analysis in primary immunodeficiency patients and healthy controls
    (WILEY, 2022) Şentürk, Gizem; Ng, Yuk Yin; Eltan, Sevgi Bilgiç; Başer, Dilek; Fırtına, Sinem
    T cell receptor excision circles (TRECs) and kappa-deleting excision circles (KRECs) are DNA fragments potentially indicative of T and B cell development, respectively. Recent thymic emigrants (RTEs) are a subset of peripheral cells that may also represent thymic function. Here, we investigated TREC/KREC copy numbers by quantitative real-time PCR in the peripheral blood of patients with primary immunodeficiencies (PIDs, n = 145) and that of healthy controls (HCs, n = 86) and assessed the correlation between RTEs and TREC copy numbers. We found that TREC copy numbers were significantly lower in children and adults with PIDs (P < .0001 and P < .002, respectively) as compared with their respective age-matched HCs. A moderate correlation was observed between TREC copies and RTE numbers among children with PID (r = .5114, P < .01), whereas no significant correlation was detected between RTE values and TREC content in the HCs (r = .0205, P = .9208). Additionally, we determined TREC and KREC copy numbers in DNA isolated from the Guthrie cards of 200 newborns and showed that this method is applicable to DNA isolated from both peripheral blood samples and dried blood spots, with the two sample types showing comparable TREC and KREC values. We further showed that RTE values are not always reliable markers of T cell output. Although additional confirmatory studies with larger cohorts are needed, our results provide thresholds for TREC/KREC copy numbers for different age groups.
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    Lymphoma predisposing gene in an extended family: CD70 signaling defect
    (Springer/Plenum Publishers, 2020) Khodzhaev, Khusan; Bay, Sema Buyukkapu; Kebudi, Rejin; Altındirek, Didem; Kaya, Ayşenur; Erbilgin, Yücel; Ng, Özden Hatırnaz; Kıykım, Ayça; Erol Çipe, Funda; Şen Zengin, Feride; Fırtına, Sinem; Ng, Yuk Yin; Aksoy, Başak Adaklı; Sayitoğlu, Müge
    Genome-wide sequencing studies in pediatric cancer cohorts indicate that about 10% of patients have germline mutations within cancer predisposition genes. Within this group, primary immune deficiencies take the priority regarding the vulnerability of the patients to infectious agents and the difficulties of cancer management. On the other hand, early recognition of these diseases may offer specific targeted therapies and hematopoietic stem cell transplantation as an option. Besides therapeutic benefits, early diagnosis will provide genetic counseling for the family members. Within this context, an extended family with multiple consanguineous marriages and affected individuals, who presented with combined immune deficiency (CID) and/or Hodgkin lymphoma phenotype, were examined by exome sequencing. A pathogenic homozygous missenseCD70variation was detected (NM_001252.5:c332C>T) in concordance withCD70phenotype and familial segregation was confirmed.CD70variations in patients with CID and malignancy have very rarely been reported. This paper reports extended family with multiple affected members with CID and malignancy carrying a missenseCD70variation, and reviews the rare cases reported in the literature. Primary immune deficiencies appear to be a potential cause for pediatric cancers. Better focusing on these inborn disorders to prevent or make an early diagnosis of malignant transformation and reduce mortalities is important.
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    Mutational landscape of severe combined immunodeficiency patients from Turkey
    (Wiley, 2020) Fırtına, Sinem; Ng, Yuk Yin; Ng, Özden Hatırnaz; Kıykım, Ayça; Aydıner, Elif; Nepesov, Serdar; Camcıoğlu, Yıldız; Sayar, Esra H.; Reisli, İsmail; Torun, Selda H.; Çöğürlü, Tuba; Uygun, Dilara; Şimşek, Işıl E.; Kaya, Ayşenur; Erol Cipe, Funda; Çağdaş, Deniz; Yücel, Esra; Çekiç, Şükrü; Uygun, Vedat; Barış, Safa; Özen, Ahmet; Özbek, Ugur; Sayitoglu, Muge
    Severe combined immunodeficiency (SCID) has a diverse genetic aetiology, where a clinical phenotype, caused by single and/or multiple gene variants, can give rise to multiple presentations. The advent of next-generation sequencing (NGS) has recently enabled rapid identification of the molecular aetiology of SCID, which is crucial for prognosis and treatment strategies. We sought to identify the genetic aetiology of various phenotypes of SCIDs and assessed both clinical and immunologic characteristics associated with gene variants. An amplicon-based targeted NGS panel, which contained 18 most common SCID-related genes, was contumely made to screen the patients (n = 38) with typical SCID, atypical SCID or OMENN syndrome. Allelic segregations were confirmed for the detected gene variants within the families. In total, 24 disease-causing variants (17 known and 7 novel) were identified in 23 patients in 9 different SCID genes: RAG1 (n = 5), RAG2 (n = 2), ADA (n = 3), DCLRE1C (n = 2), NHEJ1 (n = 2), CD3E (n = 2), IL2RG (n = 3), JAK3 (n = 4) and IL7R (n = 1). The overall success rate of our custom-made NGS panel was 60% (39.3% for NK+ SCID and 100% for NK- SCID). Incidence of autosomal-recessive inherited genes is more frequently found in our cohort than the previously reported populations probably due to the high consanguineous marriages in Turkey. In conclusion, the custom-made sequencing panel was able to identify and confirm the previously known and novel disease-causing variants with high accuracy.
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    A novel foxn1 variant is identified in two siblings with nude severe combined immunodeficiency
    (Springer/Plenum Publishers, 2019) Fırtına, Sinem; Erol Cipe, Funda; Ng, Yuk Yin; Kiykim, Ayça; Ng, Özden Hatırnaz; Sudutan, Tuğce; Aydoğmuş, Çiğdem; Barış, Safa; Öztürk, Gülyüz; Aydıner, Elif; Özen, Ahmet; Sayitoğlu, Müge
    Severe combined immunodeficiency (SCID) is the most severe form of primary immunodeficiencies (PIDs) caused by gene variants that lead to a failure of functional T cell development, with or without accompanying defects in the production of B and/or NK cells
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    Tnfrsf13b Varıants Act As Modıfıers To Clınıcal Phenotypes In Common Varıable Immune Defıcıency Dısorders
    (İstanbul Üniversitesi, 31.10.2024) Fırtına, Sinem; Kutlu, Aslı; Işıkgil, Begüm; Yozlu, Medinenur; Çepeci, Beyza Nur; Yılmaz, Hülya; Ng, Yuk Yin; Hatırnaz, Özden; Kıykım, Ayça; Özek, Esra Yücel; Aydıner, Elif; Barış, Safa; Özen, Ahmet Oğuzhan; Nepesov, Serdar; Çamcıoğlu, Yıldız; Reisli, İsmail; Ar, Muhlis Cem; Sayitoğlu, Müge
    Objective: The TNF receptor gene 13B (TNFSRF13B) is a member of the TNF superfamily which is crucial for B cell maturation, plasma cell differentiation, and antibody response. Impaired expression of the TNFRSF13B gene is associated with common variable immune deficiency (CVID), autoimmunity, and lymphoproliferation disorders. Besides the disease-causing variants of this gene, its different isoforms are associated with strong and weak TNFRSF13B expression that leads to an unbalanced B cell response. Materials and Methods: The study detected 26 variants (three synonymous, five missenses, eleven UTR, and seven intronic variants) in the TNFRSF13B gene by screening 68 CVID patients with targeted next generation sequencing. An integrative bioinformatics approach was utilized to provide a plausible explanation for CVID associations from different perspectives and to investigate the associations from the clinical findings. Results: Fifty-eight percent (15/26) of the detected variants were altered regulatory elements, such as transcription factor binding, miRNA binding sites, splice site regions or the thermodynamic impact on protein. We observed that patients who suffered from the potential splicing variants had significantly low IgA levels (p=0.009), autoimmunity (p=0.02) and gastrointestinal findings (p=0.05). In addition, the c.*79A>G 3-UTR variant was found with the low IgA and IgE levels. Thirteen variants found to have at least tenfold increased allele frequencies as compared to global databases indicating that the TNFRSF13B variants, which have a potential regulatory effect, are more common in CVID patients. Conclusions: All findings suggested that these variants may not be the causative variant for the CVID phenotype but the unbalanced TNFRSF13B alternative splices could contribute to the pathogenesis of patients independent from the underlying genetic background of CVID.